Introduction

This report documents the binning of a Nitrospira genome from the GWW sample. See Daims et al., 2015: Complete Nitrification by Nitrospira Bacteria for further details.

Load the mmgenome package

The metagenome data is analysed using the mmgenome package.

library("mmgenome")

Import data

The Rmarkdown file Load_data.Rmd describes the loading of the data and can be imported using the mmimport function. However, the preprocessed data can also be downloaded directly from figshare: Daims_GWW. Hence, here we import the prepocessed data from figshare instead.

load("Daims_GWW.RData")

Extract Nitrospira 8

As seen from the overview plots, there are numerous Nitrospira species. This one is located between multiple other species.

p <- mmplot(data = d,
            x = "HPD", 
            y = "HPF1", 
            log.x = T, 
            log.y = T, 
            color = "essential", 
            minlength = 1000,
            factor.shape = "solid") +
  scale_x_log10(limits=c(1, 10)) +
  scale_y_log10(limits=c(10, 100))

#p
#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(3.66, 4.13, 5.11, 6.32, 5.99, 4.51, 3.68),
                  HPF1  =  c(25.8, 32.4, 35.6, 30.1, 23.4, 20.3, 21.4))

mmplot_selection(p, sel)